Table 2.
Characterisation of bacterial isolates using LNC-3 probes targeting ABR genes and VF genes. LNC-3-derived signals are compared with whole genome sequencing data. Genes found in sequence data but without LNC-3 response are indicated in bold letters, LNC-3 responses that were not found via sequencing are written in italics.
| Pathogen | Detected pathogen | ABR genes | VF genes | ||
|---|---|---|---|---|---|
| Sequenced | LNC-3 | Sequenced | LNC-3 | ||
| Acinetobacter baumannii | Acinetobacter baumannii | aadA, OXA-66, SulI, Mbl abeS, adeC, adeJ, adeS, adeB, adeA, adeK, adeG, ADC-2, BlaA1, adeF, adeR, adeI, adeN, Zn-dependent hydrolase, AAC(3)-Ia, OXA-72, BlaA2 | OXA-66, SulI, Mbl abeS, adeC, adeJ, adeS, adeB, adeA, adeK, adeG, ADC-2, BlaA1, adeF, adeR, adeI, adeN, Zn-dependent hydrolase, OXA-72, BlaA2 | ||
| Enterobacter cloacae | Enterobacter cloacae | ramA, SulII, robA | ramA, SulII, robA, arnA | ||
| Enterococcus faecium | Enterococcus faecium, Enterococcus spp. | AAC(6′)-Ii, msrC, efmA | AAC(6′)-Ii, msrC, efmA, DfrG, VanA-A, VanH-A, vanRA, vanYA, TriB, aad(6) | acm | acm |
| Klebsiella pneumoniae | Klebsiella pneumoniae | oqxA, FosA5, vgaC acrA Klebsiella, oqxB | oqxA, acrA Klebsiella, oqxB | yagZ/ecpA, east1_astA | yagZ/ecpA |
| Pseudomonas aeruginosa | Multispecies probe, Pseudomonas aeruginosa | PDC-1, amrA, amrB Aph3-IIb, arnA, basS, CatB7, CpxR, MexA, MexB, MexD, MexE, MexF, mexG, mexI, mexJ, mexK, mexL, mexP, mexQ, mexV, mexW, MuxB, MuxC, OpmB, opmD, opmE, OpmH, OprJ, OprM, OXA-50, TriB, TriC, OprN, mexH, FosA, MuxA, mexM, MexC, TriA | amrA, amrB, arnA, basS, CpxR, MexB, MexD, mexG, mexI, mexJ, mexK, mexL, mexP, mexQ, mexV, OpmB, opmE, OpmH, OprJ, OprM, OXA-50, TriB, TriC, mexH, FosA, MuxA, mexM, | xcpA/pilD, algB, algQ, algZ, algU, alg8, alg44, algE, algX, algL, algF, algA, mucC, waaG, waaC, aprA, lasA, lasB, rhlI, lasI, plcH, xcpZ, xcpV, xcpT, xcpS, xcpP, xcpQ, pilY2, pilS, pilR, pilP, pilM, pilT, pilU, pilG, pilH, pilI, chpB, chpC, flgD, flgG, flgH, flgI, flgJ, fleQ, fleR, fliE, fliG, fliI, fliJ, fliM, fliN, fliP, fliQ, flhB, flhA | xcpA/pilD, algB, algQ, algZ, algU, alg8, alg44, algE, algX, algL, algF, algA, mucC, waaG, waaC, aprA, lasA, lasB, rhlI, lasI, plcH, xcpZ, xcpV, xcpS, xcpP, xcpQ, pilY2, pilR, pilP, pilT, pilU, pilG, pilI, chpB, chpC, flgD, flgG, flgH, flgI, flgJ, fleQ, fleR, , fliI, fliJ, fliM, fliN, fliP, fliQ, flhB, |
| Staphylococcus aureus | Staphylococcus aureus | Aac3-Ik, arlR, arlS, DHA-1, ErmA, FosB, MECA, mepA, mepR, mgrA, norA, sav1866, Spc, Tet-38, Aph3-III, qacA, mecR1 | Aac3-Ik, arlR, DHA-1, ErmA, FosB, MECA, mepA, mepR, mgrA, norA, sav1866, Spc, Tet-38, Aph3-III, qacA, mecR1, ACC-1 | hlgC, hlgB, ebp, sdrC, icaD, icaC, hld, hly/hla, sppC, sppB, hysA, geh, sak, hlb, adsA, scn, sdrD, sdrE, clfA, map, sea, sppA, icaA, fnbA, icaR, icaB, clfB, aur | hlgC, hlgB, ebp, sdrC, icaD, icaC, hld, hly/hla, sppC, sppB, hysA, geh, sak, hlb, adsA, scn, sdrD, sdrE, clfA, map, sea, sppA, icaA, fnbA, icaR, icaB, clfB, aur |